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Six vedeks are holding a ceremony. One of them, Latha Mabrin, is killed when the ceremonial candle issues a disruptor blast at him, throwing him back several meters and killing him instantly.

On Deep Space 9, MajorKira Nerys is examined by DoctorBashir, who complains that she hasn't been taking the makara herb he had prescribed. She complains that it tastes "like it crawled out of Quark's ear", and that it counteracts sedatives. He says that she claimed she didn't need sedatives, and she gives a weak answer. Odo then arrives and tells Kira of Latha's death, explaining that a hunter probe was hidden in the candle which was responsible for firing the disruptor blast. Unfortunately, before he became a Vedek Latha was a violent man who made no shortage of enemies leaving plenty of suspects. Kira sadly notes that despite his violent past, finding the Prophets helped him to change for the better.

On returning to her quarters, she receives a mysterious message just showing a picture of Latha, a former resistance companion of hers, as well as a distorted voice saying "That's one".

Kira reports the message to Odo and CaptainSisko, however there is no point of origin for the message so beginning an investigation is difficult. Although Kira believes it to be a general threat against the Shakaar resistance cell, none of the other members have received a message. Later, she laments to ChiefO'Brien that after everything he survived Latha would be killed during a religious ceremony. She is also frustrated as she feels she should be on Bajor taking an active role in the investigation but, as she's in the late stages of pregnancy, is left unable to do much.

Kira is then called to Ops, as she is receiving another anonymous communication. However this time it is Trentin Fala, a former ally of the resistance who is desperately paranoid that she is being watched following Latha's death. Kira decides to bring her aboard the station, and arranges for Dax and Worf (on their way back from a trip to Starbase 63) to pick her up.

Aboard their runabout, Dax and Worf discuss Jadzia mocking a Captain Ramirez for his tongo skills only to lose two bars of latinum to him having not known he was actually a champion of the game. The two debate where she'll get the money to pay him before trying to beam Fala aboard. However the transport goes badly wrong, as the buffer suddenly suffers a power surge and is unable to reconstitute her pattern. Dax and Worf desperately try to correct the problem but its no use and Fala dies painfully, leaving behind a smoking corpse.

Kira goes to see what is left of Fala's body, as Odo reports that her death was caused by a remat detonator which she had unknowingly been carrying. Although the device is typically used by the Romulans, its availability on the black market does nothing to shed any light on who is responsible. This confirms for Kira that someone is targeting the members of the Shakaar cell, revealing that although Fala wasn't officially part of the cell, she passed information to them for years while working as a cleaner in a Cardassian records office. She also notes that Fala was constantly terrified of getting caught, but never stopped helping the cell and for that, Kira considered her to be braver than any of the Shakaar's members because she lived with her fear.

Walking down the Promenade, Kira hears the same voice from before saying "That's two" and finds it coming from a PADDQuark found. Odo reasons that the killer is someone who was injured or lost family in an attack that was based on Fala's information in which Kira plays a principal role. Before they can start compiling a list, Odo's database is accessed and a picture of Mobara, another resistance companion, appears with the words "That's three". Odo immediately sends an emergency message to the university where Mobara is studying, but he can't be immediately contacted, so a search party is put together. Kira is getting more and more frustrated with everything that's happening, so Odo has her return to quarters to rest, assigning a security detachment and a personal guard to her, Lieutenant Brilgar.

However, when she arrives and heads to bed, leaving Brilgar in the living room, she hears a thud. Guessing he has just been knocked unconscious, she gets her phaser and continues to listen.

Kira opens the door and slowly peers around the dark room for the intruder. However, she finds her former Resistance colleagues Lupaza and Furel, who had broken into the O'Briens' quarters. They pledge to support her and hunt down the person responsible for the deaths of their friends. Kira tries to convince them to leave it to the authorities, but neither are happy with that solution. Lupaza then gives Kira some fresh makara herbs, and the major invites them to stay on the station. The two insist on staying near Kira, so she decides to let them stay in the quarters while Keiko and Molly are visiting Earth.

Odo reports to Captain Sisko in his office that Mobara's body was found a couple of hours earlier, the man having died when a micro-explosive planted behind his ear went off. Odo believes that the explosive was planted via a probe, since the killer clearly has expertise with remote-control devices. Although this sounds like a professional assassin, Odo notes that a professional would never send anonymous messages... this is someone with a vendetta.

In Ops, Kira and Dax enlist Nog (with his superior hearing) to help them with the messages. Upon listening, Nog notes that the messages are not complete sentences, but rather words from different speeches put together. Working from this basis, Dax assumes that as the first word is the same in all the messages then it was likely copied three times, which gives her a reference to start screening out the interference. As it starts to descramble, the three quickly recognize the voice... it's Kira's – the killer using the major's own voice in his messages.

The investigation is quickly halted when the sensors report an explosion in the habitat ring in the O'Briens' quarters, causing a hull breach. Dax puts the station to red alert and halts all traffic, as Sisko and Odo emerge from the office. Dax reports what has happened, however they suddenly realize Kira has left. The major, her fury blinding her actions, heads towards the quarters, fighting her way past all the security guards who try to stop her from exposing herself to the hull breach. Although she gets mere inches from the door panel, the baby intervenes and causes her to collapse.

In the infirmary, Kira wakes up and Bashir tells her the baby is fine and Miles wasn't in his quarters when they exploded, however Lupaza and Furel were killed. Her only comfort is that the two died instantly. Odo visits and Kira recounts her first days in the Resistance, how at the age of thirteen she'd been hanging around the cell running errands and when a planned ambush needed an extra member she volunteered. Lupaza stuck up for her despite everyone else thinking she was too small, and Shakaar decided to let her join the ambush which was a success. Afterwards she remembers how she couldn't stop smiling while Lupaza made Kira an earring from the skimmer that had just been ambushed - the one she continues to wear today - officially making Kira part of the resistance.

Kira then asks what happened, and Odo tells her that a hunter probe was attached to a freighter that docked at the station. The probe then detached and scanned each room in the habitat ring for its targets. Once it found Lupaza and Furel, it attached itself to the window and exploded. Odo has now compiled a list of twenty-five suspects who have the motive, expertise, and opportunity to commit the murders. Kira asks to see it, but Odo refuses, saying he'd like to narrow it down a little. Kira knows that Odo is worried that she'll go off on a personal vendetta mission, and tells him he's right. Odo promises to find the killer, and to keep Kira informed. As soon as he's gone however, Kira uses an emergency transport program to beam herself to the security office. There, she downloads the list to a PADD, then beams herself to a runabout. Odo enters the office a few seconds after she's gone, and notices his chair out of place. Knowing he wouldn't leave it like that, Odo asks the computer to confirm Kira's location, and it reports she's no longer on the station.

As Kira prepares to track down the killer, Odo tells Captain Sisko that Kira deleted the suspects from his database when she downloaded them so they don't know where she is headed. Sisko tells Worf to prepare the Defiant to follow the runabout, however tracking her will be difficult as Kira is masking its emissions.

After being satisfied that the first three suspects on Odo's list couldn't have been responsible for the killings, Kira visits a Cardassian named Silaran Prin living near the Demilitarized Zone. Once she beams down, Kira is stunned almost immediately by Prin.

Kira awakens to find herself restrained on a medical bed by an energy field, while Prin gravely rants about her as if she were a vile creature of darkness, "afraid of the light" which Prin fancies himself to embody. He scoffs at her accusations that he is a murderer, and insists that the former resistance members all deserved their fates.

Prin goes on to explain that he was a Cardassian civilian at the time of the Occupation, and he was burned and terribly disfigured by a bomb used to assassinate GulPirak, who had murdered fifteen Bajoran farmers who refused to display the Cardassian banner outside their homes. Fala had shown the Resistance how to circumvent his defense system, Latha built the bomb, and the device was planted on a window by Kira herself while Lupaza and Furel stood guard. The bomb was much more powerful than necessary to kill only its target, and the resulting explosion claimed twenty-three lives in total, including Gul Pirak's entire family, and injured many others who served as servants in Pirak's home, including Prin, who laundered Pirak's clothes. Prin has clearly grown more than a little insane since the attack: he continues his long monologues about darkness and light and explains that he was cautious in his murders to not hurt innocent bystanders, as he could have killed all the vedeks in the temple, Dax and Worf while aboard the runabout or half the people on Deep Space 9. Therefore, he logically intends to cut out Kira's baby, killing her and "saving" the child from being "corrupted by [her] darkness", so he can "raise it in the light". Prin feels that Kira is a murderer because she killed Cardassian civilians on Bajor along with soldiers and feels no regret for her actions. Kira responds by saying that the Cardassians had no right to be on Bajor in the first place, and for fifty years they stole food from the land while enslaving, torturing, and killing its people for profit and pleasure. Therefore all the Cardassians, from soldiers to civilians, were equally guilty and all were legitimate targets.

Prin prepares to cut out Kira's baby, but consents to administer a sedative to Kira first, to show her a level of mercy she didn't show him. When he is satisfied that the sedative has taken effect, he deactivates the restraint field and approaches, and Kira, upon whom the sedative had no effect because of the makara herbs that she has been taking lately, quickly overpowers him and kills him.

Later, when a group from DS9 arrives to rescue her, Kira is found sitting silently next to Prin's body. She is initially unresponsive, and Doctor Bashir finds a large amount of sedatives in her system, which had been counteracted by the makara herb. When she finally talks, she does so in the same manner Prin had, claiming that for all his talk of light and darkness, innocent and guilt, he hadn't realized that "the light only shines in the darkness", and "innocence is often just an excuse for the guilty". The four officers leave the grim scene, and beam up to the Defiant.

- Bashir, after the death of Trentin Fala, the latest of Kira's friends to be killed

"None of you belonged on Bajor. It wasn't your world. For fifty years you raped our planet, and you killed our people. You lived on our land and you took the food out of our mouths, and I don't care whether you held a phaser in your hand or you ironed shirts for a living. You were all guilty and you were all legitimate targets!"
"And that's what makes you a murderer. Indiscriminate killing... no sense of morality... no thought given to the consequences of your action. That's what makes us different."
"I was a soldier. You're just a bitter old man out for revenge."
"I am bringing the guilty to justice. And unlike you, I take care to protect the innocent."

- Kira and Prin

"I've made it a policy never to argue with someone's lobes."

- Dax, to Nog

"Remember Rule of Acquisition 111: 'Treat people in your debt like family... exploit them'.""You know the Rules of Acquisition?""I am a graduate of Starfleet Academy. I know many things."

-Worf and Dax

"Don't worry. I promise that I'll take care of the child and that I'll teach him the difference between darkness and light."

- Silaran Prin planning to kill Kira and remove the O'Briens unborn son from her womb

Of all the Deep Space Nine episodes Ronald D. Moore worked on, this is one of his favorites; "It really came across as I intended it, and in some ways, much better, a powerful, dark piece of television that ends in a really unexpected way." Moore particularly likes the moral ambiguity of the debate between Kira and Silaran Prin. Of this scene, he comments, "both are right and both of them are wrong." Moore was also very happy that the fact that Kira remains fundamentally Kira in the scene with Prin, that she doesn't apologize and acknowledge her own guilt. According to Moore, "typically, when you get into a scene like this in television or even film, your heroine is confronted by the man from her past who's been wronged by her in some way, and usually she'll say 'You know what? I feel bad, too. You're right. I wish I didn't have to do those things that I did. Can't we all just get along?' But that would have been so phony, especially in this situation. So I respect the fact that Kira looked at Prin and said 'Screw you! You expect me to feel sorry for you? Fifteen million Bajorans died in the Occupation. You people were on our land, you didn't belong there, and you were all guilty!' I mean that's pretty bold. You can't say whether it's right or wrong – it's the stance of a terrorist. But it's what I felt Kira absolutely believed at the core of her being." (Star Trek: Deep Space Nine Companion)

The themes touched upon in the scenes with Prin and Kira are similar to several scenes in "Duet", in which a captured war criminal confronts her about her own crimes during the Occupation.

Sisko's combadge flips above and below his grey shoulder pad in between scenes in this episode due to the mixed use of the incorrectly made jacket from "Rapture" and the new correct one that was used for the remainder of the series.

This is the first Star Trek episode to be directed by Mike Vejar since TNG: "Coming of Age", his only TNG directorial credit, almost nine years earlier in 1988. From this point onward, he remained one of the franchise's regular directors until the cancellation of Enterprise in 2005.